Photosynthesis genes and LH1 proteins of Roseospirillum parvum 930I, a purple non-sulfur bacterium with unusual spectral properties

Photosynthesis Research

Volumn 81, Issue 2, 2004, Pages 181-199

  Tuschak, Christian ^a   Beatty, J Thomas ^b   Overmann, Jörg ^a  

^a UNIVERSITY OF MUNICH   (Germany)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

3 D modeling; anoxygenic photosynthesis; evolution; light harvesting complex; pigment binding; puf genes; purple non sulfur bacteria; purple sulfur bacteria

Indexed keywords

BACTERIA (MICROORGANISMS); CHROMATIACEAE; PROKARYOTA; PROTEOBACTERIA; ROSEOSPIRILLUM; ROSEOSPIRILLUM PARVUM;

EID: 3843105698     PISSN: 01668595     EISSN: None     Source Type: Journal    
DOI: 10.1023/B:PRES.0000035046.91126.bd     Document Type: Article

References (69)

1. Alberti M, Burke DH and Hearst JE (1995) Structure and sequence of the photosynthesis gene cluster. In: Blankenship RE, Madigan MT and Bauer CE (eds) Anoxygenic Photosynthetic Bacteria, pp 1083-1106. Kluwer Academic Publishers, Dordrecht, The Netherlands
2. Altschul SF, Madden TL, Schäffer AA, Zhang J, Miller W and Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402
3. Beja O, Suzuki MT, Heidelberg JF, Nelson WC, Preston CM, Hamada T, Eisen JA, Fraser CM and DeLong EF (2002) Unsuspected diversity among marine aerobic anoxygenic phototrophs. Nature 415: 630-633
4. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA and Wheeler DL (2002) GenBank. Nucleic Acids Res 30: 17-20
5. Broveak T (1996) GeneWorks. Biotechnol Software Internet J 13: 11-14
6. Choudhary M and Kaplan S (2000) DNA sequence analysis of the photosynthesis region of Rhodobacter sphaeroides 2.4.1. Nucleic Acids Res 28: 862-867
7. Cogdell RJ, Isaacs NW, Freer AA, Arrelano J, Howard TD, Papiz MZ, Hawthornwaite-Lawless AM and Prince SM (1997) The structure and function of the LH2 (B800-850) complex from the purple photosynthetic bacterium Rhodopseudomonas acidophila strain 10050. Prog Biophys Mol Biol 68: 1-27
8. Cogdell RJ, Isaacs NW, Howard TD, McLuskey K, Fraser NJ and Prince SM (1999) How photosynthetic bacteria harvest solar energy. J Bacteriol 181: 3869-3879
9. y absorption band of bacteriochlorophyll a in purple bacterial antenna complexes. Photosynth Res 74: 135-141
10. Conroy MJ, Westerhuis WHJ, Parkes-Loach PS, Loach PA, Hunter CN and Williamson MP (2000) The solution structure of Rhodobacter sphaeroides LH1 beta reveals two helical domains separated by a more flexible region: structural consequences for the LH1 complex. J Mol Biol 298: 83-94
11. Corson GE, Nagashima KVP, Matsuura K, Sakuragi Y, Wettasinghe R, Qin H, Allen R and Knaff DB (1999) Genes encoding light-harvesting and reaction center proteins from Chromatium vinosum. Photosynth Res 59: 39-52
12. Dayhoff MO, Schwartz RM and Orcutt BC (1979) A model of evolutionary change in proteins. In: Dayhoff MO (ed) Atlas of Protein Sequence and Structure pp 345-352. National Biomedical Research Foundation, Silver Spring, Maryland
13. Douglas SE (1995) DNA Strider - an inexpensive sequence-analysis package for the Macintosh. Mol Biotechnol 3: 37-45
14. Eccles J and Honig B (1983) Charged amino acids as spectroscopic determinants for chlorophyll in vivo. Proc Natl Acad Sci 80: 4959-4962
15. Fathir I, Ashikaga M, Tanaka K, Katano T, Nirasawa T, Kobayashi M, Wang Z-Y and Nozawa T (1998) Biochemical and spectral characterization of the core light harvesting complex 1 (LH1) from the thermophilic purple sulfur bacterium Chromatium tepidum. Photosynth Res 58: 193-202
16. Felsenstein J (2002) PHYLIP, Phylogeny Inference Package, Version 3.6(alpha3). Retrieved from http://evolution.genetics.washington.edu/phylip. html. Department of Genome Sciences, University of Washington, Seattle, Washington
17. Fitch WM and Margoliash E (1967) Construction of phylogenetic trees: a method based on mutation distances as estimated from cytochrome c sequences is of general applicability. Science 155: 279-284
18. Frese RN, Olsen JD, Branvall R, Westerhuis WHJ, Hunter CN and van Grondelle R (2000) The long-range supraorganization of the bacterial photosynthetic unit: a key role for PufX. Proc Natl Acad Sci 97: 5197-5202
19. Garcia D, Parot P, Vermeglio A and Madigan MT (1986) The light-harvesting complexes of a thermophilic purple sulfur photosynthetic bacterium Chromatium tepidum. Biochim Biophys Acta 850: 390-395
20. Germeroth L, Lottspeich F, Robert B and Michel H (1993) Unexpected similarities of the B800-850 light-harvesting complex from Rhodospirillum molischianum to the B870 light-harvesting complexes from other purple photosynthetic bacteria. Biochemistry 32: 5615-5621
21. Giraud E, Hannibal L, Fardoux J, Vermeglio A and Dreyfus B (2000) Effect of Bradyrhizobium photosynthesis in stem nodulation of Aeschynomene sensitiva. Proc Natl Acad Sci 97: 14795-14800
22. Glaeser J and Overmann J (1999) Selective enrichment and characterization of Roseospirillum parvum, gen. nov and sp. nov., a new purple nonsulfur bacterium with unusual light absorption properties. Arch Microbiol 171: 405-416
23. Gudowska-Nowak E, Newton MD and Fajer J (1990) Conformational and environmental effects on bacteriochlorophyll optical spectra: correlations of calculated spectra with structural results. J Phys Chem 94: 5795-5801
24. Guex N and Peitsch MC (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18: 2714-2723 (http://www.expasy.ch/spdbv/)
25. Guex N, Diemand A and Peitsch MC (1999) Protein modelling for all. Trends Biochem Sci 24: 364-367
26. Hanson LK, Thompson MA and Fajer J (1987) Environmental effects on the properties of chlorophylls in vivo. Theoretical models. In: Biggins J (ed) Progress in Photosynthesis Research, pp 311-314. Martinus Nijhoff, Dordrecht, The Netherlands
27. Hunter CN (1995) Genetic manipulation of the antenna complexes of purple bacteria. In: Blankenship RE, Madigan MT and Bauer CE (eds) Anoxygenic Photosynthetic Bacteria, pp 473-501. Kluwer Academic Publishers, Dordrecht, The Netherlands
28. Igarashi N, Harada J, Nagashima S, Matsuura K, Shimada K and Nagashima KVP (2001) Horizontal transfer of the photosynthesis gene cluster and operon rearrangement in purple bacteria. J Mol Evol 52: 333-341
29. Jamieson SJ, Wang P, Qian P, Kirkland JY, Conroy MJ, Hunter CN and Bullough PA (2002) Projection structure of the photosynthetic reaction centre-antenna complex of Rhodospirillum rubrum at 8.5 Å resolution. EMBO J 21: 3927-3935
30. Jukes TH and Cantor CR (1969) Evolution of protein molecules. In: Munro HM (ed) Mammalian Protein Metabolism, pp 21-132. Academic Press, New York
31. Karrasch S, Bullough PA and Gosh R (1995) The 8.5 Å projection map of the light-harvesting complex I from Rhodospirillum rubrum reveals a ring composed of 16 subunits. EMBO J 14: 631-638
32. Koepke J, Hu XC, Muenke C, Schulten K and Michel H (1996) The crystal structure of the light-harvesting complex II (B800-850) from Rhodospirillum molischianum. Structure 4: 581-597
33. Kortluke C, Breese K, Gadon N, Labahn A and Drews G (1997) Structure of the puf operon of the obligately aerobic, bacteriochlorophyll a containing bacterium Roseobacter denitrificans OCh114 and its expression in a Rhodobacter capsulatus puf puc deletion mutant. J Bacteriol 179: 5247-5258
34. Loach PA (2000) Supramolecular complexes in photosynthetic bacteria. Proc Natl Acad Sci 97: 5016-5018
35. Loach PA and Parkes-Loach PS (1995) Structure-function relationships in core light-harvesting complexes (LHI) as determined by characterization of the structural subunit and by reconstitution experiments. In: Blankenship RE, Madigan MT and Bauer CE (eds) Anoxygenic Photosynthetic Bacteria, pp 437-471. Kluwer Academic Publishers, Dordrecht, The Netherlands
36. Marck C (1988) DNA Strider - a C-program for the fast analysis of DNA and protein sequences on the Apple Macintosh family of computers. Nucleic Acids Res 16: 1829-1836
37. McDermott G, Prince SM, Freer AA, Hawthornwaite-Lawless AM, Papiz MZ, Cogdell RJ and Isaacs NW (1995) Crystal structure of an integral membrane light-harvesting complex from photosynthetic bacteria. Nature 374: 517-521
38. McLuskey K, Prince SM, Cogdell RJ and Isaacs NW (2001) The crystallographic structure of the B800-820 LH3 light-harvesting complex from the purple bacteria Rhodopseudomonas acidophila strain 7050. Biochemistry 40: 8783-8789
39. Nagashima KVP, Matsuura K and Shimada K (1996) The nucleotide sequence of the puf operon from the purple photosynthetic bacterium, Rhodospirillum molischianum: comparative analyses of light-harvesting proteins and the cytochrome subunits associated with the reaction centers. Photosynth Res 50: 61-70
40. Nagashima KVP, Shimada K and Matsuura K (1993) Phylogenetic analysis of photosynthetic genes of Rhodocyclus gelatinosus: possibility of horizontal gene transfer in purple bacteria. Photosynth Res 36: 185-191
41. Nagashima KVP, Hiraishi A, Shimada K and Matsuura K (1997a) Horizontal transfer of genes coding for the photosynthetic reaction centers of purple bacteria. J Mol Evol 45: 131-136
42. Nagashima KVP, Matsuura K, Wakao N, Hiraishi A and Shimada K (1997b) Nucleotide sequences of genes coding for photosynthetic reaction centers and light-harvesting proteins of Acidiphilium rubrum and related aerobic acidophilic bacteria. Plant Cell Physiol 38: 1249-1258
43. Naylor GW, Addlesee HA, Gibson LCD and Hunter CN (1999) The photosynthesis gene cluster of Rhodobacter sphaeroides. Photosynth Res 62: 121-139
44. Nicholas KB and Nicholas HBJ (1997) GeneDoc: analysis and visualization of genetic variation. Retrieved from http:// www.psc.edu/biomed/genedoc
45. Ochman H, Medhora MM, Garza D and Hartl DL (1990) Amplification of flanking sequences by inverse PCR. In: PCR Protocols: a Guide to Methods and Applications, pp 219-227. Academic Press, San Diego, California
46. Ochman H, Ayala FJ and Hartl DL (1993) Use of polymerase chain reaction to amplify segments outside boundaries of known sequences. Meth Enzymol 218: 309-321
47. Olsen JD, Sockalingum GD, Robert B and Hunter CN (1994) Modification of a hydrogen bond to a bacteriochlorophyll a molecule in the light-harvesting 1 antenna of Rhodobacter sphaeroides. Proc Natl Acad Sci 91: 7124-7128
48. Olsen JD, Sturgis JN, Westerhuis WHJ, Fowler GJS, Hunter CN and Robert B (1997) Site-directed modification of the ligands to the bacteriochlorophylls of the light-harvesting LH1 and LH2 complexes of Rhodobacter sphaeroides. Biochemistry 36: 12625-12632
49. Papiz MZ, Prince SM, Hawthornwaite-Lawless AM, McDermott G, Freer AA, Isaacs NW and Cogdell RJ (1996) A model for the photosynthetic apparatus of purple bacteria. Trends Plant Sci 1: 198-206
50. Papiz MZ, Prince SM, Howard T, Cogdell RJ and Isaacs NW (2003) The structure and thermal motion of the B800-850 LH2 complex from Rps. acidophila at 2.0 Å resolution and 100K: new structural features and functionally relevant motions. J Mol Biol 326: 1523-1538
51. Permentier HP (2001) Light-harvesting and core complexes of anoxygenic phototrophic bacteria. PhD Thesis, pp 36-40. Department of Biophysics, Leiden University, Leiden
52. Permentier HP, Neerken S, Schmidt KA, Overmann J and Amesz J (2000) Energy transfer and charge separation in the purple non-sulfur bacterium Roseospirillum parvum. Biochim Biophys Acta 1460: 338-345
53. Permentier HP, Neerken S, Overmann J and Amesz J (2001) A bacteriochlorophyll a antenna complex from purple bacteria absorbing at 963 nm. Biochemistry 40: 5573-5578
54. Prince SM, Papiz MZ, Freer AA, McDermott G, Hawthornwaite-Lawless AM, Cogdell RJ and Isaacs NW (1997) Apoprotein structure in the LH2 complex from Rhodopseudomonas acidophila strain 10050: modular assembly and protein pigment interactions. J Mol Biol 268: 412-423
55. Raymond J, Zhaxybayeva O, Gogarten JP, Gerdes SY and Blankenship RE (2002) Whole-genome analysis of photosynthetic prokaryotes. Science 298: 1616-1620
56. Roszak AW, Howard TD, Southall J, Gardiner AT, Law CJ, Isaacs NW and Cogdell RJ (2003) Crystal structure of the RC-LH1 core complex from Rhodopseudomonas palustris. Science 302: 1969-1972
57. Sambrook J, Fritsch EF and Maniatis T (1989) Molecular Cloning: a Laboratory Manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
58. Scheuring S, Francia F, Busselez J, Melandri BA, Rigaud J-L and Levy D (2004) Structural role of PufX in the dimerization of the photosynthetic core complex of Rhodobacter sphaeroides. J Biol Chem 279: 3620-3626
59. Siebert CA, Qian P, Fotiadis D, Engel A, Hunter CN and Bullough PA (2004) Molecular architecture of photosynthetic membranes in Rhodobacter sphaeroides: the role of PufX. EMBO J 23: 690-700
60. Sorgen PL, Cahill SM, Krueger-Koplin RD, Krueger-Koplin ST, Schenck CC and Girvin ME (2002) Structure of the Rhodobacter sphaeroides light-harvesting 1 beta subunit in detergent Micelles. Biochemistry 41: 31-41
61. Sturgis JN, Olsen JD, Robert B and Hunter CN (1997) Functions of conserved tryptophan residues of the core light-harvesting complex of Rhodobacter sphaeroides. Biochemistry 36: 2772-2778
62. Suyama T, Shigematsu T, Takaichi S, Nodasaka Y, Fujikawa S, Hosoya H, Tokiwa Y, Kanagawa T and Hanada S (1999) Roseateles depolymerans gen. nov., sp. nov., a new bacteriochlorophyll a-containing obligate aerobe belonging to the beta-subclass of the proteobacteria. Int J Syst Bacteriol 49: 449-457
63. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F and Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882
64. Wagner-Huber R, Brunisholz RA, Bissig I, Frank G, Suter F and Zuber H (1992) The primary structure of the antenna polypeptides of Ectothiorhodospira halochloris and Ectothiorhodospira halophila. Four core-type antenna polypeptides in E. halochloris and E. halophila. Eur J Biochem 205: 917-925
65. Walz T, Jamieson SJ, Bowers CM, Bullough PA and Hunter CN (1998) Projection structures of three photosynthetic complexes from Rhodobacter sphaeroides: LH2 at 6 Å, LH1 and RC-LH1 at 25 Å. J Mol Biol 282: 833-845
66. Yurkov VV and Beatty JT (1998) Aerobic anoxygenic phototrophic bacteria. Microbiol Mol Biol Rev 62: 695-724
67. Zuber H and Brunisholz RA (1991) Structure and function of antenna polypeptides and chlorophyll-protein complexes: principles and variability. In: Scheer H (ed) Chlorophylls, pp 627-703. CRC Press, Boca Raton, Florida
68. Zuber H and Cogdell RJ (1995) Structure and organization of purple bacterial antenna complexes. In: Blankenship RE, Madigan MT and Bauer CE (eds) Anoxygenic Photosynthetic Bacteria, pp 315-348. Kluwer Academic Publishers, Dordrecht, The Netherlands
69. Zuker M, Mathews DH and Turner DH (1999) Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide. In: Barciszewski J and Clark BFC (eds) RNA Biochemistry and Biotechnology, pp 11-43. Kluwer Academic Publishers, Dordrecht, The Netherlands